concatenate_runs: Sum the reads/gene for multiple sequencing runs of a single...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Sum the reads/gene for multiple sequencing runs of a single condition/batch.

Description

On occasion we have multiple technical replicates of a sequencing run. This can use a column in the experimental design to identify those replicates and sum the counts into a single column in the count tables.

Usage

concatenate_runs(expt, column = "replicate")

Arguments

expt	Experiment class containing the requisite metadata and count tables.
column	Column of the design matrix used to specify which samples are replicates.

Details

Untested as of 2016-12-01, but used in a couple of projects where sequencing runs got repeated.

Value

Expt with the concatenated counts, new design matrix, batches, conditions, etc.

See Also

[Biobase] [exprs()] [fData()] [pData()] [create_expt()]

Examples

## Not run: 
 compressed <- concatenate_runs(expt)

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.